Man pages for strandCheckR
Calculate strandness information of a bam file
| calculateStrandCoverage | Calculate the strand information based on coverage |
| calculateStrandNbReads | Calculate the strand information based the number of reads |
| checkPairedEnd | Test whether a bam file if single end or paired end |
| concatenateAlignments | Concatenate a list of Alignments into One |
| filterDNA | Filter Double Strand Sequences from a Bam File |
| getWinFromBamFile | get the strand information of all windows from bam files |
| getWinFromGranges | Get the Sliding Windows from a GRanges object |
| getWinFromIRanges | Get the Ranges of Sliding Windows from an IRanges object |
| getWinFromReadInfo | get the strand information of all windows from read... |
| getWinOfAlignments | get the window ranges of alignments |
| intersectWithFeature | Intersect the windows data frame with an annotation data... |
| keptProbaWin | get the probability of begin kept for each window |
| keptReadFragment | calculate the read fragments to be kept |
| plotHist | Plot the histogram of positive proportions |
| plotWin | Plot the Proportion of + Stranded Reads |
| strandCheckR-package | Quantify and Filter putative double strand DNA from... |
| summarizeHist | Summarize the histogram of strand proportions from the input... |
